Oh, well. Then you'll need to but CN, I personally also have a N3DS and CN and it works just fine, but yeah your only option is CN. Unless someone makes a version that is compatible with gateways MSET on N3DS, but as there are fairly little people interested in it it probably won't happen.

For GBA games you need to be in sysNAND not emuNAND (i.e. not in "Gateway Mode").

Only sysNAND, with signature checks patched out, which means CFW. And to run CFW (e.g. Pasta CFW), you need an entry point. Currently, Ninjhax, via Cubic Ninja. Maybe when someone releases a port of the MSET exploit, like what Gateway uses. Then you'll only need Cubic Ninja (or a Sky3DS with Cubic Ninja on it) only once, until you downgrade the Settings app. Then you'll just go to Settings -> Profile -> Nintendo DS Profile to start the CFW. There probably is someone working on it, but nothing made public yet.